I do prefer boat diving given the choice over shore. It would also depend on location location location .. They are completely two different worlds. Not all shore dives are created equal and same for boat dives. To many variables to name. ...
Some key factors for both are: Biggest factor is location ( CA vs FL or HI ) !!!
Shore dives: access, parking, facilities, waves, distance to dive (surface swim), visibility, float, fun etc..
Boat Dive: cost, crew, boat, crowds, time, better spots, food, service, safety support (DM +emergency first aid on board), extra eyes, boat access only dive sites, fun, etc..
Comes down to preferences and availability.